Depending on the type of analyzer you have on your GC instrument, this won't necessarily be a 1:1 relationship between two different compounds. The relationship for each individual compound is proportional to the number of moles of that compound. Typically GCs use a combustion analysis to measure what is coming off of the column. Therefore, the area under the peak will depend on the particular molecule that is being combusted; in general larger molecules will give a greater peak area because more heat is released in their combustion. The way to solve this problem is to make a 1:1 mixture of two compounds and measure the areas you get from the GC trace of the mixture. Then, since you know that there was an equal number of moles of each compound, you can figure out the proportion that relates the area of the two peaks. This can allow you to calculate the yield of your reaction based just on the GC trace!

Note that in most cases you can assume that the relation between the two different compounds is 1:1, but if you want precise results you should figure out the relation I described.

I bet this sounds complicated. Sorry if I didn't explain it very well.

Movies has explained this greatly, but I wanted to add this one. "Internal standard technique" is frequently used for quantification, in which a known amount of substance is added and whose peak is known to occur far from the analyte peaks. So, comparing the peak areas with analyte peaks, a quantification is very easy to calculate.

Chem_tr makes a good point. When using internal standards it is also important that the internal standard be unreactive under the conditions of the reaction you are monitoring. High molecular weight n-alkanes are therefore good for this purpose. I frequently use tridecane.